Alignment output chromosome number replaced with contig ID
Summary
Chromosome numbers not being saved, instead it is the contig ID... this is evident in all the bams, but goes all the way back to sam...
Steps to reproduce
Look at the output of any alignData step and do a head -n 5
on the sam
Observed bug behavior
Instead of chr1 it lists chrNC_000001.11
Expected behavior
See above
Relevant logs and/or screenshots
Potential fixes
This is either a problem with the reference or the hisat2 command